Resampling-based confidence regions and multiple tests for a correlated random vector

We derive non-asymptotic confidence regions for the mean of a random vector whose coordinates have an unknown dependence structure. The random vector is supposed to be either Gaussian or to have a symmetric bounded distribution, and we observe $n$ i.i.d copies of it. The confidence regions are built using a data-dependent threshold based on a weighted bootstrap procedure. We consider two approaches, the first based on a concentration approach and the second on a direct boostrapped quantile approach. The first one allows to deal with a very large class of resampling weights while our results for the second are restricted to Rademacher weights. However, the second method seems more accurate in practice. Our results are motivated by multiple testing problems, and we show on simulations that our procedures are better than the Bonferroni procedure (union bound) as soon as the observed vector has sufficiently correlated coordinates.Comment: submitted to COL

Marine benthic flora and fauna of Gourdon Bay and the Dampier Peninsula in the Kimberley region of North-Western Australia

Surveys undertaken to characterise the marine benthic habitats along the Dampier Peninsula and further south at Gourdon Bay in the Kimberley region of Western Australia were augmented with epibenthic sled sampling of soft and hard bottom habitats. This paper describes the species collected, their biomass and relative abundance for the main groups of marine macrophytes and invertebrates. Five localities were surveyed; Gourdon Bay, Quondong Point to Coulomb Point, Carnot Bay to Beagle Bay, Perpendicular Head and Packer Island. Sampling was limited to fifteen epibenthic dredge operations from a range of habitat types and was designed to target the most common habitat types and to obtain species identifications of the most important species and those which typified different habitat types. Surveys covered a total of 1,350 m 2 of seabed in depths between 11 and 23m. We identified 415 taxa comprising: 1 seagrass, 43 algae, 52 sponges, 30 ascidians, 10 hydroids, 14 scleractinian corals, 52 other cnidarians, 69 crustaceans, 73 molluscs and 71 echinoderms. Despite the limited nature of the sampling, a significant number of new species, range extensions and new records for Western Australia and Australia were recorded. Within the algae, one range extension (Halimeda cf. cuneata f. digitata not previously recorded in Western Australia) and one possible new species of Areschougia were recorded. Two range extensions were present in the ascidians; the solitary ascidian Polycarpa cf. intonata has previously only been recorded in Queensland and Cnemidocarpa cf. radicosa only in temperate Australian waters. There were several range extensions for the crustacea, for example, the sponge crab, Tumidodromia dormia, has only been recorded in Queensland. One species of holothurian of the genus Phyllophorus could not be identified from the literature available and may represent a new species. Similarly, a small species of the echinoid Gymnechinus could possibly be a new species. The collections of hydroids, hard corals, crinoids and molluscs contained no new species or range extensions. There was difficulty in identification of some groups to species level due to the status of the current taxonomic literature (e.g. Cnidaria, Porifera and ascidians) and there may be a number of new species among the material collected. Among the anthozoa, there is at least one new species of Chromonephthea and potentially 10 range extensions to Western Australia. Sinularia cf. acuta and Chromonephthea curvata are both new records for Australia with both previously recorded in Indonesia only. Among the better known taxa (e.g. molluscs, echinoderms, corals), most of the taxa identified to species level have been recorded to occur throughout north-western Australia, however the diversity recorded in this study is less than other parts of the Kimberley and this is almost certainly a result of the small overall area sampled and the single method of collection utilised. The most important species on soft bottom habitats in terms of biomass was the heart urchin Breynia desorii (up to 326 g.m -2). Sponges were the dominant fauna by biomass (up to 620 g.m -2) on hard bottom habitats and biomass was dominated a by a few large cup and massive sponge species (e.g. Pione velans and two unidentified Spheciospongia). The biomass of other filter feeders, especially ascidians (e.g. Aplidium cf. crateriferum), soft corals (e.g. Chromonephthea spp.), gorgonians (e.g. Junceella fragilis and Dichotella gemmacea) was also high, indicating the importance of these groups in characterising hard bottom habitats. Although low in biomass, crinoids such as Comaster multifidus and Comatula pectinata were abundant in samples that included a high biomass of other filter feeders

Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks

The idea of 'date' and 'party' hubs has been influential in the study of protein-protein interaction networks. Date hubs display low co-expression with their partners, whilst party hubs have high co-expression. It was proposed that party hubs are local coordinators whereas date hubs are global connectors. Here we show that the reported importance of date hubs to network connectivity can in fact be attributed to a tiny subset of them. Crucially, these few, extremely central, hubs do not display particularly low expression correlation, undermining the idea of a link between this quantity and hub function. The date/party distinction was originally motivated by an approximately bimodal distribution of hub co-expression; we show that this feature is not always robust to methodological changes. Additionally, topological properties of hubs do not in general correlate with co-expression. Thus, we suggest that a date/party dichotomy is not meaningful and it might be more useful to conceive of roles for protein-protein interactions rather than individual proteins. We find significant correlations between interaction centrality and the functional similarity of the interacting proteins.Comment: 27 pages, 5 main figures, 4 supplementary figure

Atmospheric Escape From Three Terrestrial Planets in the L 98-59 System

A critically important process affecting the climate evolution and potential habitability of an exoplanet is atmospheric escape, in which high-energy radiation from a star drives the escape of hydrogen atoms and other light elements from a planet's atmosphere. L 98-59 is a benchmark system for studying such atmospheric processes, with three transiting terrestrial-size planets receiving Venus-like instellations (4-25 S$_\oplus$) from their M3 host star. We use the VPLanet model to simulate the evolution of the L 98-59 system and the atmospheric escape of its inner three small planets, given different assumed initial water quantities. We find that, regardless of their initial water content, all three planets accumulate significant quantities of oxygen due to efficient water photolysis and hydrogen loss. All three planets also receive enough XUV flux to drive rapid water loss, which considerably affects their developing climates and atmospheres. Even in scenarios of low initial water content, our results suggest that the James Webb Space Telescope (JWST) will be sensitive to observations of retained oxygen on the L 98-59 planets in its future scheduled observations, with planets b and c being the most likely targets to possess an extended atmosphere. Our results constrain the atmospheric evolution of these small rocky planets, and they provide context for current and future observations of the L 98-59 system to generalize our understanding of multi-terrestrial planet systems.Comment: 17 pages, 7 figures, accepted for publication in the Astrophysical Journa

Toxoplasma seroprevalence in a rural population in France: detection of a household effect

<p>Abstract</p> <p>Background</p> <p><it>Toxoplasma gondii</it>, the agent of toxoplasmosis, has a complex life cycle. In humans, the parasite may be acquired either through ingestion of contaminated meat or through oocysts present in the environment. The importance of each source of contamination varies locally according to the environment characteristics and to differences concerning human eating habits and the presence of cats; thus, the risk factors may be determined through fine-scale studies. Here, we searched for factors associated with seropositivity in the population of two adjacent villages in Lorraine region, France.</p> <p>Methods</p> <p>All voluntary inhabitants filled out a questionnaire and gave a blood sample. The seroprevalence was estimated globally and according to the inhabitants' ages using a cubic spline regression. A mixed logistic regression model was used to quantify the effect of individual and household factors on the probability of seropositivity.</p> <p>Results</p> <p>Based on serological results from 273 persons, we estimated seroprevalence to be 47% (95% confidence interval: 41 to 53%). That seroprevalence increased with age: the slope was the steepest up to the age of 40 years (OR = 2.48 per 10-year increment, 95% credibility interval: [1.29 to 5.09]), but that increase was not significant afterwards. The probability of seropositivity tended to be higher in men than in women (OR = 2.01, 95% credibility interval: [0.92 to 4.72]) and in subjects eating raw vegetables at least once a week than in the others (OR = 8.4, 95% credibility interval: [0.93 to 72.1]). These effects were close to statistical significance. The multivariable analysis highlighted a significant seroprevalence heterogeneity among households. That seroprevalence varied between 6 and 91% (5^thand 95^thpercentile of the household seropositivity distribution).</p> <p>Conclusion</p> <p>The major finding is the household effect, with a strong heterogeneity of seroprevalence among households. This effect may be explained by common exposures of household members to local risk factors. Future work will quantify the link between the presence of oocysts in the soil and the seroprevalence of exposed households using a spatial analysis.</p

Gauge-theoretic invariants for topological insulators: A bridge between Berry, Wess-Zumino, and Fu-Kane-Mele

We establish a connection between two recently-proposed approaches to the understanding of the geometric origin of the Fu-Kane-Mele invariant $\mathrm{FKM} \in \mathbb{Z}_2$, arising in the context of 2-dimensional time-reversal symmetric topological insulators. On the one hand, the $\mathbb{Z}_2$ invariant can be formulated in terms of the Berry connection and the Berry curvature of the Bloch bundle of occupied states over the Brillouin torus. On the other, using techniques from the theory of bundle gerbes it is possible to provide an expression for $\mathrm{FKM}$ containing the square root of the Wess-Zumino amplitude for a certain $U(N)$-valued field over the Brillouin torus. We link the two formulas by showing directly the equality between the above mentioned Wess-Zumino amplitude and the Berry phase, as well as between their square roots. An essential tool of independent interest is an equivariant version of the adjoint Polyakov-Wiegmann formula for fields $\mathbb{T}^2 \to U(N)$, of which we provide a proof employing only basic homotopy theory and circumventing the language of bundle gerbes.Comment: 23 pages, 1 figure. To appear in Letters in Mathematical Physic

Rhomboid family member 2 regulates cytoskeletal stress-associated Keratin 16.

Keratin 16 (K16) is a cytoskeletal scaffolding protein highly expressed at pressure-bearing sites of the mammalian footpad. It can be induced in hyperproliferative states such as wound healing, inflammation and cancer. Here we show that the inactive rhomboid protease RHBDF2 (iRHOM2) regulates thickening of the footpad epidermis through its interaction with K16. K16 expression is absent in the thinned footpads of irhom2-/- mice compared with irhom2+/+mice, due to reduced keratinocyte proliferation. Gain-of-function mutations in iRHOM2 underlie Tylosis with oesophageal cancer (TOC), characterized by palmoplantar thickening, upregulate K16 with robust downregulation of its type II keratin binding partner, K6. By orchestrating the remodelling and turnover of K16, and uncoupling it from K6, iRHOM2 regulates the epithelial response to physical stress. These findings contribute to our understanding of the molecular mechanisms underlying hyperproliferation of the palmoplantar epidermis in both physiological and disease states, and how this 'stress' keratin is regulated

Interaction of eukaryotic translation initiation factor 4G with the nuclear cap-binding complex provides a link between nuclear and cytoplasmic functions of the m7 guanosine cap

In eukaryotes the majority of mRNAs have an m7G cap that is added cotranscriptionally and that plays an important role in many aspects of mRNA metabolism. The nuclear cap-binding complex (CBC; consisting of CBP20 and CBP80) mediates the stimulatory functions of the cap in pre-mRNA splicing, 3' end formation, and U snRNA export. As little is known about how nuclear CBC mediates the effects of the cap in higher eukaryotes, we have characterized proteins that interact with CBC in HeLa cell nuclear extracts as potential mediators of its function. Using cross-linking and coimmunoprecipitation, we show that eukaryotic translation initiation factor 4G (eIF4G), in addition to its function in the cytoplasm, is a nuclear CBC-interacting protein. We demonstrate that eIF4G interacts with CBC in vitro and that, in addition to its cytoplasmic localization, there is a significant nuclear pool of eIF4G in mammalian cells in vivo. Immunoprecipitation experiments suggest that, in contrast to the cytoplasmic pool, much of the nuclear eIF4G is not associated with eIF4E (translation cap binding protein of eIF4F) but is associated with CBC. While eIF4G stably associates with spliceosomes in vitro and shows close association with spliceosomal snRNPs and splicing factors in vivo, depletion studies show that it does not participate directly in the splicing reaction. Taken together the data indicate that nuclear eIF4G may be recruited to pre-mRNAs via its interaction with CBC and accompanies the mRNA to the cytoplasm, facilitating the switching of CBC for eIF4F. This may provide a mechanism to couple nuclear and cytoplasmic functions of the mRNA cap structure